|
| Status |
Public on Aug 01, 2017 |
| Title |
Mono_day 10 batch2 |
| Sample type |
SRA |
| |
|
| Source name |
CD34-positive HSC induced to monocytic differentiation for 10 days
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: Monocytic middle stage
tissue: hematopoietic systerm
batch: batch2
|
| Treatment protocol |
G-CSF and M-CSF
|
| Growth protocol |
IMDM+FBS+IL-3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol reagent
polyA-enriched RNA
illumina RNA-seq library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
CD34-positive HSC induced to monocytic differentiation for 10 days
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trim Galore v0.3.7 with parameters -q 25 --stringency 5 --length 50 --paired --phred33, and filtered for low-quality sequence, then mapped to hg38 whole genome of GENCODE v25 using tophat v2.1.0 with parameters -p 14 --splice-mismatches 1 --segment-mismatches 2 --mate-inner-dist 50 --mate-std-dev 20 --library-type fr-unstranded
Non-normalized raw counts were calculated using featureCounts v1.5.0 with parameters -T 7 --primary. In short, exons from all isoforms of a gene were merged to create one meta-transcript. Fragments Per Kilobase of exon model per Million (FPKM) mapped reads were calculated using cufflinks v2.2.1 with parameters -p 10 -u --library-type fr-unstranded -G gencode.v24.annotation.gtf.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include non-normalized raw counts and FPKM values for each Sample.
|
| |
|
| Submission date |
Sep 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jia Yu |
| E-mail(s) |
j-yu@ibms.pumc.edu.cn
|
| Organization name |
Peking Union Medical College
|
| Street address |
Dong Dan San Tiao 5, Dongcheng District
|
| City |
Beijing |
| ZIP/Postal code |
100005 |
| Country |
China |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE87088 |
KSRP specifies monocytic and granulocytic differentiation through regulating miR-129 biogenesis and RUNX1 expression |
|
| Relations |
| BioSample |
SAMN05788805 |
| SRA |
SRX2175641 |
